Structural and thermodynamic insights into the coordination preference of norbornadiene with the initiator complex [RuCl2(PPh3)2(piperidine)] in polymerization via olefin metathesis.

The metathesis reaction has been an important tool in both organic and inorganic synthetic chemistry. More specifically in polymer chemistry, ring opening metathesis polymerization (ROMP), via the formation of an active metal-carbene species (MCHR), has been widely used. The elucidation of the mechanism for ROMP opened the way for the development of well-defined catalysts, suited to local conditions. In the present study, we employed density functional theory (DFT) to investigate three reaction pathways for the formation of a species capable of activating ROMP. The active species is formed from the [RuCl2(PPh3)2(pip)] complex in the presence of norbornadiene (NBD) and the carbene source ethyl diazoacetate (EDA). Formation of a hexacoordinated intermediate [RuCl2(PPh3)2(pip)(NBD)] is favored in the first step, with NBD doubly coordinated to the [RuCl2(PPh3)2(pip)] moiety. Analysis of donation (X → Ru) and back-donation (Ru → X) processes in the [RuCl2(PPh3)2(pip)(NBD)] complex shows that piperidine behaves as a σ donor, while NBD behaves as a π donor and the PPh3 groups act as π acceptors. The intensity of the orbital component is predominant in relation to the steric component in the complex. Thus, we propose that the reaction occurs through the formation of a hexacoordinated complex, followed by the dissociation of a PPh3 group, thus forming a complex where NBD is doubly coordinated to the metal center. Coordination of EDA leads finally to the catalyst capable of forming the metallocyclobutane intermediate required for the ROMP reaction.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride.

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Revisiting the structure of Heliannuol L: A computational approach.

Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of 1 H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively.

A DFT study of the interaction between [Cd(H2O)3]2+ and monodentate O-, N-, and S-donor ligands: bond interaction analysis.

A series of B3LYP/6-311+G(d,p) calculations of the affinity of monodentate ligands for [Cd(H2O)3]2+ are performed. Three types of ligands containing O (phosphine oxide, lactam, amide, carboxylic acid, ester, ketone, aldehyde, ether, halohydrin, enol, furan), N (thiocyanate, amine, ammonia, azide), and S (thioester, thioketone, thiol, thiophene, disulfide) interacting atoms are investigated. The results show that phosphine oxide has the largest affinity for the cadmium cation due to the polarization of the P=O bond. As the P atom has a large atomic radius, the O atom can polarize the electronic cloud enhancing its amount of electronic charge and favoring the interaction with Cd2+. The affinity order found is phosphine oxide > thioester > lactam > amide > carboxylic acid > ester > thioketone > ketone > thiocyanate > amine > ammonia > aldehyde > ether > thiol > thiophene > enol > halohydrin > disulfide > azide > furan ligands. These results were also corroborated by the functional M06-2X. The electronic effects (resonance and induction) of neighboring groups of the interacting atom modulate the strength of metal-ligand binding. For almost all the O-donor ligands the electrostatic component has the same magnitude as the covalent term, while for the N- and S-donor ligands the covalent term is predominant. The polarization term accounts for twice the exchange term as part of the covalent component. The dispersion term varies less than 2 kcal mol-1 for the complexes analyzed. The Pauli repulsion term is correlated with the metal ligand distance, increasing in the compounds with decreased metal-ligand bond length. The charge between the interacting atoms is also strongly correlated with both the interacting strength and the electrostatic interaction component. The natural bond orbital analysis highlights correlations of the bond order, and S and P contributions of the interacting metal-ligand orbital with the coordination strength. Graphical abstract The affinity of 20 monodentate ligands with different functional groups for the [Cd(H2O)3]2+ cation is calculated based on the interaction enthalpy and Gibbs free energy for the substitution of one water molecule from the fully hydrated cation. The affinity is correlated with geometric, electronic, and energetic parameters of the ligands and the complexes as well as with energy decomposition and natural bond order analyses results.

Insights into the interactions of CO2 with amines: a DFT benchmark study.

The interaction between CO2 and 1,2-diaminoethane was computed using pure and hybrid density functionals. The CAM-B3LYP and wB97X-D functionals using a triple-ζ basis set that includes diffuse and polarization functions are the best functionals for calculating the relative energies of the zwitterion intermediate compared to a coupled-cluster with a single, double and non-iterative triple excitation (CCSD(T)) approach extrapolated to a complete basis set limit. With the two functionals and the triple-ζ basis set, the zwitterion is 1.70 kcal mol(-1) less stable than the reactants, and close to 1.63 kcal mol(-1) computed using the CCSD(T) approach. The inclusion of vibrational and thermal corrections and of entropic effects increases the relative energy of the zwitterion to 14.7 kcal mol(-1). Bending of the CO2 geometry increases its acidity due to a 1.09 eV reduction in the LUMO energy. Calculation of the CO2 interaction energy with a set of amines revealed that the interaction energies show a high correlation with their basicities, with the stronger bases stabilizing the zwitterion. For the most basic amine computed (3,4,6,7,8,9-hexahydro-2H-pyrimido[1,2-a]pyrimidine), the Gibbs free energy of the zwitterion is 15.8 kcal mol(-1) lower than the reactants. Therefore, for this highly basic amine, the zwitterion may have a longer lifetime, in contrast to 2-aminoethanol (MEA), where it is only a transient species.

Interaction between alkaline earth cations and oxo-ligands. DFT study of the affinity of the Ca2+ cation for carbonyl ligands.

The affinity of the Ca(2+) ion for a set of substituted carbonyl ligands was analyzed with both the DFT (B3LYP/6-31+G(d)) and semi-empirical (PM6) methods. Two types of ligands were studied: a set of monosubstituted [O=CH(R)] and a set of disubstituted ligands [O=C(R)(2)] (R=H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either directly bound to the carbonyl carbon atom or to the para position of a phenyl ring. The interaction energy was calculated to quantify the affinity of the Ca(2+) cation for the ligands. Geometric and electronic parameters were correlated with the intensity of the metal-ligand interaction. The electronic nature of the substituent is the main parameter that determines the interaction energy. Donor groups make the interaction energy more negative (stabilizing the complex formed), while acceptor groups make the interaction energy less negative (destabilizing the complex formed).

Aminequinone-hydroxylquinoneimine tautomeric equilibrium revisited: molecular modeling study of the tautomeric equilibrium and substituent effects in 4-(4-R-phenylamino)naphthalene-1,2-diones.

Semi-empirical (AM1 and PM3) and DFT (B3LYP/6-31G(d)) calculations were employed to study the tautomeric equilibrium between the aminequinone A and hydroxylquinoneimine B forms of 4-(4-R-phenylamino)naphthalene-1,2-diones. Substituent effects on the tautomeric equilibrium as well as on geometric and electronic parameters were also determined. In the gas phase the hydroxylquinoneimine B form is the most stable, whereas in water the aminequinone A form becomes more stable. The substituents do not modify the relative energies of the two tautomers. These results are in accordance with experimental data reported in the literature.

Interaction between artemisinin and heme. A Density Functional Theory study of structures and interaction energies.

Malaria is an infectious disease caused by the unicellular parasite Plasmodium sp. Currently, the malaria parasite is becoming resistant to the traditional pharmacological alternatives, which are ineffective. Artemisinin is the most recent advance in the chemotherapy of malaria. Since it has been proven that artemisinin may act on intracellular heme, we have undertaken a systematic study of several interactions and arrangements between artemisinin and heme. Density Functional Theory calculations were employed to calculate interaction energies, electronic states, and geometrical arrangements for the complex between the heme group and artemisinin. The results show that the interaction between the heme group and artemisinin at long distances occurs through a complex where the iron atom of the heme group retains its electronic features, leading to a quintet state as the most stable one. However, for interaction at short distances, due to artemisinin reduction by the heme group, the most stable complex has a septet spin state. These results suggest that a thermodynamically favorable interaction between artemisinin and heme may happen.